13-108306732-AT-A

Position:

• chr13-108306732-AT-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006573.5(TNFSF13B):​c.746-84del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000977 in 584,348 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000054 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0013 (1 hom.)
• Consequence: TNFSF13B NM_006573.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

TNFSF13B (HGNC:11929): (TNF superfamily member 13b) The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This cytokine is a ligand for receptors TNFRSF13B/TACI, TNFRSF17/BCMA, and TNFRSF13C/BAFFR. This cytokine is expressed in B cell lineage cells, and acts as a potent B cell activator. It has been also shown to play an important role in the proliferation and differentiation of B cells. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFSF13B	NM_006573.5	c.746-84del		intron_variant		ENST00000375887.9	NP_006564.1
TNFSF13B	NM_001145645.2	c.689-84del		intron_variant			NP_001139117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFSF13B	ENST00000375887.9	c.746-84del		intron_variant		1	NM_006573.5	ENSP00000365048	P1
TNFSF13B	ENST00000430559.5	c.689-84del		intron_variant		1		ENSP00000389540
TNFSF13B	ENST00000493765.1	n.300-84del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0000536 AC: 8 AN: 149322 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000735

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000420

Gnomad FIN AF: 0.000204

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000149

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00129 AC: 563 AN: 435026 Hom.: 1 AF XY: 0.00130 AC XY: 299 AN XY: 229822

Gnomad4 AFR exome AF: 0.000654

Gnomad4 AMR exome AF: 0.00120

Gnomad4 ASJ exome AF: 0.00131

Gnomad4 EAS exome AF: 0.000466

Gnomad4 SAS exome AF: 0.00187

Gnomad4 FIN exome AF: 0.00171

Gnomad4 NFE exome AF: 0.00128

Gnomad4 OTH exome AF: 0.00115

GnomAD4 genome AF: 0.0000536 AC: 8 AN: 149322 Hom.: 0 Cov.: 0 AF XY: 0.0000550 AC XY: 4 AN XY: 72784

Gnomad4 AFR AF: 0.0000735

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000420

Gnomad4 FIN AF: 0.000204

Gnomad4 NFE AF: 0.0000149

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11381410; hg19: chr13-108959080;